Polymer ejection from strong spherical confinement

Piili, Joonas; Linna, Riku

doi:10.1103/physreve.92.062715

Cited by 9 publications

(29 citation statements)

References 31 publications

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“…t w (s) is defined as the time it takes for a monomer labeled s to translocate after the previous monomer s − 1 has translocated. From our simu- * Author to whom correspondence should be addressed: riku.linna@aalto.fi lations using a hybrid method consisting of molecular dynamics (MD) and stochastic rotation dynamics (SRD) [11,12] we obtained t w that grows essentially exponentially with s [13].…”

Section: Introductionmentioning

confidence: 99%

Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics

2017

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We use stochastic rotation dynamics to examine the dynamics of the ejection of an initially strongly confined flexible polymer from a spherical capsid with and without hydrodynamics. The results obtained using SRD are compared to similar Langevin simulations. Inclusion of hydrodynamic modes speeds up the ejection but also allows the part of the polymer outside the capsid to expand closer to equilibrium. This shows as higher values of radius of gyration when hydrodynamics are enabled. By examining the waiting times of individual polymer beads we find that the waiting time tw grows with the number of ejected monomers s as a sum of two exponents. When ≈ 63% of the polymer has ejected the ejection enters the regime of slower dynamics. The functional form of tw vs s is universal for all ejection processes starting from the same initial monomer densities. Inclusion of hydrodynamics only reduces its magnitude. Consequently, we define a universal scaling function h such that the cumulative waiting time t = N0h(s/N0) for large N0. Our unprecedently precise measurements of force indicate that this form for tw(s) originates from the corresponding force towards the pore decreasing super exponentially at the end of the ejection. Our measured tw(s) explains the apparent superlinear scaling of the ejection time with the polymer length for short polymers. However, for asymptotically long polymers tw(s) predicts linear scaling.

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Section: Introductionmentioning

confidence: 99%

Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics

2017

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“…Using our general simulation model, we will study the ejection process for polymers of different bending rigidity. In our previous studies on capsid ejection of flexible polymers we showed that the ejection dynamics is governed by the force the polymer beads inside the capsid exert on the bead at the pore entrance [14,15]. As will be seen, this result cannot be generalized to semiflexible polymer chains.…”

Section: Introductionmentioning

confidence: 93%

“…As κ increases, there is a transition from exponential increase of t with s [14,15] to a regime where perfect scaling of t ∼ s 1.33 emerges for the main part of the ejection. This transition has the characteristics of a dynamical phase transition, where κ acts as a control parameter.…”

Section: E Cumulative Waiting Times: Cross-over To Scalingmentioning

confidence: 99%

“…This way we ensure that polymers of different lengths are packaged in a consistent way. For fully flexible polymers waiting times t w (s) (i.e., the time it takes for bead s to eject the capsid the last time after bead s − 1 has ejected the capsid the last time) reflect the force f (s) measured at the pore [14,15]. To see if this is the case also for semiflexible polymers we measure f (s).…”

Section: Creating Initial Polymer Conformationsmentioning

confidence: 99%

“…Accordingly, also capsid ejection of polymers has been the subject of a number of theoretical treatments [5][6][7][8][9]. These theoretical treatments have been accompanied by a multitude of studies using computer simulations [10][11][12][13][14][15][16]. These studies have addressed the ejection of fully flexible polymers and as such provide important information on the fundamentals of ejection dynamics.…”

Section: Introductionmentioning

confidence: 99%

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Rigidity-induced scale invariance in polymer ejection from capsid

2017

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While the dynamics of a fully flexible polymer ejecting a capsid through a nanopore has been extensively studied, the ejection dynamics of semiflexible polymers has not been properly characterized. Here we report results from simulations of ejection dynamics of semiflexible polymers ejecting from spherical capsids. Ejections start from strongly confined polymer conformations of constant initial monomer density. We find that, unlike for fully flexible polymers, for semiflexible polymers the force measured at the pore does not show a direct relation to the instantaneous ejection velocity. The cumulative waiting time t(s), that is, the time at which a monomer s exits the capsid the last time, shows a clear change when increasing the polymer rigidity κ. The major part of an ejecting polymer is driven out of the capsid by internal pressure. At the final stage the polymer escapes the capsid by diffusion. For the driven part there is a crossover from essentially exponential growth of t with s of the fully flexible polymers to a scale-invariant form. In addition, a clear dependence of t on polymer length N_{0} was found. These findings combined give the dependence t(s)∝N_{0}^{0.55}s^{1.33} for the strongly rigid polymers. This crossover in dynamics where κ acts as a control parameter is reminiscent of a phase transition. This analogy is further enhanced by our finding a perfect data collapse of t for polymers of different N_{0} and any constant κ.

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Spontaneous Injection of Polymer into a Spherical Cavity from a Narrow Tube

Wang

Zhao

et al. 2020

Macromolecules

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The spontaneous injection of a polymer chain into a spherical cavity from a narrow cylindrical tube is investigated by using Monte Carlo simulation. A continuous phase transition from a partially injected state to a completely injected state is found at the critical radius (R C ) of the spherical cavity. The dependence of R C on the polymer length (N) and the radius of tube (r) can be described by a scaling relation R C ∝ N 1/3 r 1−1/3ν with ν as the Flory exponent. In the partially injected phase, the number of injected monomers (m in ) in the sphere can be written as m in ∝ R 3 r (1−3ν)/ν , in good agreement with the results from the free energy landscape. The injection time (τ) for the polymer ejecting from the tube is a function of R and behaves differently for the partially injected phase and the completely injected phase, which can be described qualitatively by a simple kinetic model.

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Polymer ejection from strong spherical confinement

Cited by 9 publications

References 31 publications

Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics

Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics

Rigidity-induced scale invariance in polymer ejection from capsid

Spontaneous Injection of Polymer into a Spherical Cavity from a Narrow Tube

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